This directory contains the Apis mellifera Amel_1.2 assembly
(apiMel1, Jul. 2004) from the Baylor College of Medicine HGSC Honey
Bee Genome Project. For more information, see the Baylor website:
http://www.hgsc.bcm.tmc.edu/projects/honeybee/.
Files included in this directory:
md5sum.txt - Checksums of the files in this directory.
apiMel1.2bit - contains the complete A. mellifera/apiMel1 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
scaffoldFa.zip - The working draft sequence in one file per scaffold.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are in lower case while non-repeating sequence is
in upper case. The main assembly is in the chrN.fa files where N
is the name of the scaffold.
scaffoldFaMasked.zip - The working draft sequence in one file per
scaffold. Repeats are masked by capital Ns and non-repeating
sequence is shown in upper case.
scaffoldOut.zip - RepeatMasker .out file for scaffolds. These were
created with RepeatMasker at the -s sensitive setting.
scaffoldTrf.zip - Tandem Repeats Finder locations, filtered to keep
repeats with period less than or equal to 12, translated into one
.bed file per scaffold.
apiMel1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/apiMel1/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
For conditions of use regarding these data, see
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html.